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Yorodumi- PDB-3to0: Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) C... -
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-Basic information
Entry | Database: PDB / ID: 3to0 | ||||||
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Title | Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) C217A, C239A bound to FMN | ||||||
Components | Iodotyrosine deiodinase 1 | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / MEMBRANE / TRANSMEMBRANE / DEHALOGENASE / IODIDE SALVAGE / MONO-IODOTYROSINE / NADP | ||||||
Function / homology | Function and homology information Thyroxine biosynthesis / iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / thyroid hormone metabolic process / cytoplasmic vesicle membrane / FMN binding / oxidoreductase activity / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.655 Å | ||||||
Authors | Buss, J.M. / McTamney, P.M. / Rokita, S.E. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Expression of a soluble form of iodotyrosine deiodinase for active site characterization by engineering the native membrane protein from Mus musculus. Authors: Buss, J.M. / McTamney, P.M. / Rokita, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3to0.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3to0.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 3to0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3to0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3to0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3to0_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3to0_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/3to0 ftp://data.pdbj.org/pub/pdb/validation_reports/to/3to0 | HTTPS FTP |
-Related structure data
Related structure data | 3tnzC 3gb5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 29923.273 Da / Num. of mol.: 2 / Mutation: C217A, C239A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: 10090 / Gene: IYD-1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9DCX8, EC: 1.22.1.1 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M ammonium acetate 0.1M Bis-Tris pH 6.0, 45% v/v 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Mar 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.655→19.88 Å / Num. obs: 15404 / % possible obs: 99.71 % / Redundancy: 3.7 % / Rsym value: 0.105 / Net I/σ(I): 73 |
Reflection shell | Resolution: 2.656→2.75 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.81 / Num. unique all: 1493 / Rsym value: 0.534 / % possible all: 80.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GB5 Resolution: 2.655→19.88 Å / SU ML: 0.95 / σ(F): 1.96 / Phase error: 22.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.424 Å2 / ksol: 0.394 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.655→19.88 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | T13: 0.0027 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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